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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| README.txt | 2012-07-11 | 1.9 kB | |
| PE.pl.gz | 2012-07-11 | 1.5 kB | |
| Preprocess_rm0to22.pl.gz | 2012-07-11 | 1.3 kB | |
| Preprocess_rm_normal.pl.gz | 2012-07-11 | 1.3 kB | |
| links.pl.gz | 2012-07-11 | 2.2 kB | |
| Totals: 5 Items | 8.1 kB | 0 | |
README ________________________________________________________________________ These perl scripts are associated with the manuscript "A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing". Please find brief descriptions, usage information and module requirements below. ________________________________________________________________________ PE.pl PE.pl is a script that simulates paired end sequencing data and writes fastq files in the Illumina format. It selects random positions in the user-provided genome, normalized for different chromosome lengths. User-defined parameters include the number of read pairs, read length, mean insert size and standard deviation. Requirements: Math::Random Usage: perl PE.pl <seq_files_extension> <number_of_readpairs> <readlength> <mean_insert_size> <st_deviation> <output_file_prefix> ________________________________________________________________________ links.pl links.pl takes the SVDetect (http://svdetect.sourceforge.net) "linking" output file (*.links) as input, searches for "imperfect duplicates" (reads with 1-2 bp offset in coordinates) and outputs a modified *.links file with imperfect duplicates removed. The script requires three arguments: (1) The read length, (2) the input filename, and (3) the output filename. ________________________________________________________________________ Preprocess_rm0to22.pl Preprocess_rm_normal.pl Preprocess_rm0to22.pl and Preprocess_rm_normal.pl are scripts that modify BWA sam files. Preprocess_rm0to22.pl removes all read pairs where one or both reads in a pair have mapping qualities 0-22. Preprocess_rm_normal.pl removes concordant read pairs. Usage: Preprocess_rm_normal.pl <file.sam> Output file with extension .rm_normal.sam is produced. Preprocess_rm0to22.pl <file.sam> Output file with extension .rm0to22.sam is produced.